maximum number of files for running oligomer in the command line?

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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rubenmartinez
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Location: Centro de Investigacion del Cancer, Salamanca, Spain

maximum number of files for running oligomer in the command line?

#1 Post by rubenmartinez » 2021.10.22 17:45

Hello,
I am running oligomer (ATSAS 3.0.3; r12736) in the command line of MacOS over multiple files (oligomer -brief -ff formfactors.dat -dat *.dat) and it stops after processing 80 files with this message:

> sg&?5??@f??? e??? T??h?: parse error

This has happened already with 3 different datasets.
I wonder whether there is a maximum number of files to be batch processed in the command line? In this case, is there any way to increase this number?
Thank you!
Best regards,
Ruben

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biosaxs.com
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maximum number of files for running oligomer: 50

#2 Post by biosaxs.com » 2021.10.29 12:25

Thank you for reporting this.
Currently, OLIGOMER cannot handle more than 50 experimental data files or more than 50 form factors. Please organize your input data in groups of 50 files or less and run OLIGOMER on each group separately. The 'oligomer.log' will be appended, not overwritten.
Apologies for the inconvenience.

rubenmartinez
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Posts: 4
Joined: 2012.01.17 19:21
Location: Centro de Investigacion del Cancer, Salamanca, Spain

Re: maximum number of files for running oligomer in the command line?

#3 Post by rubenmartinez » 2021.10.29 12:55

Thank you for your reply!
In case this might be helpful for someone else, I solved this issue by writting a small script that runs over all the data files in a folder:

for f in *; do
/path_to_oligomer/oligomer -brief -ff ../my_ff_data.dat -dat $f -out=oligomer_0.log ;
done

but, please, do not laugh at my scripting abilities. I perfectly know I'm not a nerd! :lol: :P :D
Best wishes,
Ruben

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